Especially on a 947' ship, Finney could barely squeeze his head into it!

There's also the issue of reloading the pod after use (without having to go outside the ship). Rather than have a section of the ships who's sole purpose is to prep and jettison ion pods (a rare need) it makes much more sense to have a multi-role system.

Timo - I agree that if it's merely being jettisoned (rather than launched, as I alluded to) then perhaps a "kick it out the back" setup might be preferable.
In which case, there are any number of hatches along the bottom of the secondary hull that could house the neccessary machinery.